In order to break through the technological monopoly of ultra-deep water well control and riser system abroad and form a certain independent design situation, the ultra-deep water well control and riser system applied in drilling ship is studied. Taking a drilling ship project as an example, the design and layout optimization of ultra-deep water well control and riser system are carried out from the aspects of hydraulic control system of blowout preventer and diverter, well control ultrahigh pressure test system, ultra-deep water well control and riser system layout and movement. The design and layout of the ultra-deep water well control and riser system are reasonable through the actual ship layout and the completed test. Compared with the original design and layout, the optimized scheme solves the problem of the difficult placement of related equipment on the drilling ship, and has the advantages of extending the service life of the control fluid, optimizing the diverter’s overflow piping / the operating process of the pressure test system and saving time, flexibly switching the lower riser assembly and the lower BOP storage and pressure test, and simplifying the movement process of related equipment. The design and layout optimization scheme of the system can provide valuable reference for the design or construction of subsequent similar drilling equipment.